Changeset 5020

Timestamp:

Sep 2, 2021 4:10:06 PM (2 years ago)

Author:

toby

Message:

index changes for CCTBX; new scrolled output routine; document external routines

Location:

trunk

Files:

• GSASIIctrlGUI.py (modified) (2 diffs)
• GSASIIindex.py (modified) (6 diffs)
• docs/source/packages.rst (modified) (2 diffs)

trunk/GSASIIctrlGUI.py

@@ -82 +82 @@
                                    used in Bind elsewhere in the code.
 :func:`G2MessageBox`               Displays text typically used for errors or warnings. 
+:func:`ShowScrolledInfo`           Displays longer text where scrolling is possibly needed
 :func:`GetItemOrder`               Creates a dialog for ordering items into columns
 :func:`GetImportFile`              Gets one ore more file from the appropriate import
@@ -2412 +2413 @@
     dlg.ShowModal()
     dlg.Destroy()
+
+def ShowScrolledInfo(parent,txt,width=600,height=400,header='Warning info'):
+    '''Simple code to display possibly extensive error or warning text
+    in a scrolled window.
+
+    :param wx.Frame parent: parent window for 
+    :param str txt: text to be displayed
+    :param int width: lateral of window in pixels (defaults to 600)
+    :param int height: vertical dimension of window in pixels (defaults to 400)
+    :param str header: width of window in pixels (defaults to 600)
+    '''
     
+    dlg = wx.Dialog(parent.GetTopLevelParent(),wx.ID_ANY,header, style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER)
+    spanel = wxscroll.ScrolledPanel(dlg, wx.ID_ANY, size=(width-20, height))
+    mainSizer = wx.BoxSizer(wx.VERTICAL)
+    mainSizer.Add(spanel,1,wx.ALL|wx.EXPAND,1)
+
+    txtSizer = wx.BoxSizer(wx.VERTICAL)
+    txt = wx.StaticText(spanel,wx.ID_ANY,txt)
+    txt.Wrap(600)
+    txt.SetBackgroundColour(wx.WHITE)
+    txtSizer.Add(txt,1,wx.ALL|wx.EXPAND,1)
+    spanel.SetSizer(txtSizer)
+    btnsizer = wx.BoxSizer(wx.HORIZONTAL)
+    btn = wx.Button(dlg, wx.ID_CLOSE) 
+    btn.Bind(wx.EVT_BUTTON,lambda event: dlg.EndModal(wx.ID_CANCEL))
+    btnsizer.Add(btn)
+    mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER|wx.ALL, 5)
+    dlg.SetSizer(mainSizer)
+    mainSizer.Fit(dlg)
+    spanel.SetAutoLayout(1)
+    spanel.SetupScrolling()
+    #dlg.SetMaxSize((-1,400)) 
+    dlg.CenterOnParent()
+    dlg.ShowModal()
+    dlg.Destroy()
+
 ################################################################################
 class PickTwoDialog(wx.Dialog):

trunk/GSASIIindex.py

@@ -832 +832 @@
     return len(HKL),M20,X20,A
         
-def findBestCell(dlg,ncMax,A,Ntries,ibrav,peaks,V1,ifX20=True):
+def findBestCell(dlg,ncMax,A,Ntries,ibrav,peaks,V1,ifX20=True,cctbx_args=None):
     'needs a doc string'
 # dlg & ncMax are used for wx progress bar 
@@ -871 +871 @@
         
         if IndexPeaks(peaks,HKL)[0] and len(HKL) > mHKL[ibrav]:
-            Lhkl,M20,X20,Aref = refinePeaks(peaks,ibrav,Abeg,ifX20)
+            Lhkl,M20,X20,Aref = refinePeaks(peaks,ibrav,Abeg,ifX20,cctbx_args=cctbx_args)
             Asave.append([calc_M20(peaks,HKL,ifX20),Aref[:]])
             if ibrav in [9,10,11]:                          #A,B,or C-centered orthorhombic
                 for i in range(2):
                     Abeg = rotOrthoA(Abeg[:])
-                    Lhkl,M20,X20,Aref = refinePeaks(peaks,ibrav,Abeg,ifX20)
+                    Lhkl,M20,X20,Aref = refinePeaks(peaks,ibrav,Abeg,ifX20,cctbx_args=cctbx_args)
                     HKL = G2lat.GenHBravais(dmin,ibrav,Aref)
                     peaks = IndexPeaks(peaks,HKL)[1]
@@ -882 +882 @@
             # elif ibrav == 15:                      #C-centered monoclinic
             #     Abeg = swapMonoA(Abeg[:])
-            #     Lhkl,M20,X20,Aref = refinePeaks(peaks,ibrav,Abeg,ifX20)
+            #     Lhkl,M20,X20,Aref = refinePeaks(peaks,ibrav,Abeg,ifX20,cctbx_args=cctbx_args)
             #     HKL = G2lat.GenHBravais(dmin,ibrav,Aref)
             #     peaks = IndexPeaks(peaks,HKL)[1]
@@ -892 +892 @@
     X = sortM20(Asave)
     if X:
-        Lhkl,M20,X20,A = refinePeaks(peaks,ibrav,X[0][1],ifX20)
+        Lhkl,M20,X20,A = refinePeaks(peaks,ibrav,X[0][1],ifX20,cctbx_args=cctbx_args)
         return GoOn,Skip,Lhkl,M20,X20,A        
     else:
@@ -959 +959 @@
 
 def DoIndexPeaks(peaks,controls,bravais,dlg,ifX20=True,
-            timeout=None,M20_min=2.0,X20_max=None,return_Nc=False):
+            timeout=None,M20_min=2.0,X20_max=None,return_Nc=False,
+            cctbx_args=None):
     'needs a doc string'
     
@@ -1010 +1011 @@
                                 if not N2:
                                     A = []
-                                    GoOn,Skip,Nc,M20,X20,A = findBestCell(dlg,ncMax,A,Nm[ibrav]*N1s[ibrav],ibrav,peaks,V1,ifX20)
+                                    GoOn,Skip,Nc,M20,X20,A = findBestCell(dlg,ncMax,A,Nm[ibrav]*N1s[ibrav],ibrav,peaks,V1,ifX20,cctbx_args=cctbx_args)
                                     if Skip:
                                         break
                                 if A:
-                                    GoOn,Skip,Nc,M20,X20,A = findBestCell(dlg,ncMax,A[:],N1s[ibrav],ibrav,peaks,0,ifX20)
+                                    GoOn,Skip,Nc,M20,X20,A = findBestCell(dlg,ncMax,A[:],N1s[ibrav],ibrav,peaks,0,ifX20,cctbx_args=cctbx_args)
                             else:
-                                GoOn,Skip,Nc,M20,X20,A = findBestCell(dlg,ncMax,0,Nm[ibrav]*N1s[ibrav],ibrav,peaks,V1,ifX20)
+                                GoOn,Skip,Nc,M20,X20,A = findBestCell(dlg,ncMax,0,Nm[ibrav]*N1s[ibrav],ibrav,peaks,V1,ifX20,cctbx_args=cctbx_args)
                             if Skip:
                                 break

trunk/docs/source/packages.rst

@@ -51 +51 @@
   GSAS-II to download updates to our code.
 
-
 Scripting  Requirements
 -----------------------
@@ -65 +64 @@
 http://www.pythonware.com/products/pil/), or h5py + hdf5 to function
 but scripts will load and run without these. 
+
+
+External and Supplied Programs
+--------------------------------
+
+GSAS-II provides interfaces to use a number of programs developed by
+others. Some are included with GSAS-II and others must be installed
+separately. When these programs are accessed, citation
+information is provided. 
+
+GSAS-II includes copies of these programs:
+
+  **DIFFaX**
+    Simulate layered structures with faulting
+    
+  **CifFile**
+    A software library used to read data and structures from CIF
+    
+  **Shapes**
+    Model small angle scattering with shaped particles
+    
+  **NIST FPA**
+    Use Fundamental Parameters to determine GSAS-II profile function 
+
+No additional steps beyond a standard installation
+are needed to access their functionality.
+
+**Bilboa Crystallographic Server**: GSAS-II directly access the
+Bilboa Crystallographic Server (provided
+the computer has internet access). This allows automated use of the
+k-SUBGROUPSMAG, k-SUBGROUPS and PseudoLattice web utilities for
+computation of space group subgroups, color (magnetic) subgroups &
+lattice search.
+
+At the request of the program authors, these programs are not included
+with GSAS-II and must be installed separately:
+
+  **RMCProfile**
+    Large-box PDF & S(Q) fitting. We have heard from users that V6.7.7
+    of RMCProfile is compatible with the input created by GSAS-II,
+    but not V6.7.9.
+
+  **fullrmc**
+    A modern software toolkit for large-box PDF & S(Q) fitting. Use
+    version 5.0 or later. 
+
+  **Dysnomia**
+    Computes enhanced Fourier maps with Maximum Entropy estimated
+    extension of reflection sphere